Contacts of the strand formed by residues 297 - 305 (chain A) in PDB entry 5TWV


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 297 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  GLY*     3.1    15.9    -      -       -      +
    290A  VAL*     3.5    26.9    -      -       +      -
    295A  GLY      3.6     4.2    +      -       -      +
    296A  ILE*     1.3    82.8    -      -       -      +
    298A  THR*     1.3    60.9    +      -       -      +
    211C  ILE*     4.4    18.6    -      -       -      +
    290C  VAL*     3.9    26.7    -      -       -      +
    291C  VAL      5.1     4.2    +      -       -      +
    292C  GLU*     5.2     4.3    -      -       -      +
    295C  GLY*     5.7     1.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  ALA*     3.4    28.2    +      -       +      +
    175A  HIS*     4.3     7.3    +      -       -      -
    177A  ARG*     5.1     3.6    -      -       +      -
    178A  ALA*     3.0    36.4    -      -       +      +
    181A  LEU*     4.9     7.9    -      -       +      -
    210A  ILE*     5.6     6.1    -      -       +      -
    287A  LEU      3.9     0.3    -      -       -      +
    288A  GLU*     3.5     5.1    -      -       -      +
    289A  GLY*     2.8    36.1    +      -       -      +
    290A  VAL*     5.8     2.0    -      -       -      -
    291A  VAL*     6.0     1.6    -      -       +      +
    296A  ILE      4.0     1.9    +      -       -      +
    297A  THR*     1.3    74.4    -      -       -      +
    299A  GLN*     1.3    70.2    +      -       -      +
    211C  ILE*     4.7     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  HIS*     5.9     0.7    +      -       -      -
    178A  ALA*     4.2     5.1    -      -       -      +
    286A  ILE*     3.4    19.0    -      -       +      +
    287A  LEU      3.2    23.1    -      -       -      +
    288A  GLU*     3.9    17.7    -      -       +      +
    298A  THR*     1.3    85.9    +      -       -      +
    300A  ALA*     1.3    88.1    +      -       -      +
    301A  ARG*     2.9    54.1    +      -       -      +
    209C  MET*     5.6     0.3    -      -       -      +
    211C  ILE*     3.9    28.9    -      -       +      +
    250C  PHE*     4.1     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  ALA*     4.3    11.4    -      -       +      +
    181A  LEU*     4.2    28.0    -      -       +      +
    183A  PHE*     3.8    19.4    -      -       +      -
    285A  VAL      3.6     1.7    -      -       -      +
    287A  LEU*     2.9    31.8    +      -       +      +
    299A  GLN*     1.3    85.4    +      -       -      +
    301A  ARG*     1.3    58.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     5.0     6.5    -      -       +      -
     39A  LYS      3.2     4.2    +      -       -      +
     40A  GLY*     3.2    31.3    -      -       -      -
     41A  ASN*     3.8    31.4    -      -       -      +
     42A  CYS*     4.4    12.4    -      -       -      -
    183A  PHE*     4.5     0.2    -      -       -      -
    284A  ILE*     6.3     1.8    -      -       +      -
    285A  VAL      3.3    11.7    -      -       -      +
    286A  ILE*     5.2     1.8    -      -       +      -
    299A  GLN*     2.9    47.7    +      -       -      +
    300A  ALA*     1.3    74.1    -      -       -      +
    302A  THR*     1.3    73.9    +      -       -      +
    209C  MET*     4.5    14.5    -      -       -      +
    211C  ILE*     5.8     2.0    -      -       -      +
    250C  PHE*     3.9    23.3    -      -       +      -
    292C  GLU*     4.6    14.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     4.4     4.3    -      -       -      -
     37A  SER      4.0     7.2    -      -       -      -
     38A  LYS*     3.3    28.3    -      -       +      +
     39A  LYS      4.2     4.7    -      -       -      +
    183A  PHE*     3.3    38.5    -      -       +      -
    284A  ILE*     3.5     6.4    -      -       -      +
    285A  VAL*     2.9    42.8    +      -       -      +
    301A  ARG*     1.3    84.9    -      -       -      +
    303A  SER*     1.3    63.9    +      -       -      +
    304A  TYR*     3.9     9.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ARG*     4.9     4.2    +      -       -      -
     36A  VAL*     3.2    32.3    -      -       -      -
     37A  SER      4.1     4.9    +      -       -      -
     38A  LYS*     4.9     7.1    -      -       -      +
    282A  GLU*     2.8    35.4    +      -       -      +
    283A  ILE      3.5    11.1    +      -       -      -
    284A  ILE*     3.6     8.1    -      -       -      +
    302A  THR*     1.3    74.8    -      -       -      +
    304A  TYR*     1.3    67.3    +      -       -      +
    305A  LEU*     4.1     4.3    -      -       -      +
    308A  GLU*     3.0    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LYS*     5.7     1.8    -      -       +      -
    183A  PHE*     3.6    10.1    -      +       +      +
    184A  SER*     2.6    42.8    +      -       -      -
    185A  LYS      3.6    12.6    -      -       -      -
    186A  HIS      3.9    12.8    -      -       -      -
    187A  ALA*     4.1    16.8    -      -       +      -
    198A  PHE*     5.6     2.7    -      -       +      -
    200A  LEU*     3.9    21.2    -      -       +      +
    201A  ARG      5.4     0.2    +      -       -      -
    281A  LEU*     5.6     0.7    -      -       -      +
    282A  GLU*     3.9     3.2    -      -       -      -
    283A  ILE*     3.1    32.0    +      -       +      +
    285A  VAL*     3.9    18.2    -      -       +      -
    302A  THR*     3.9    20.9    -      -       -      -
    303A  SER*     1.3    78.1    -      -       -      +
    305A  LEU*     1.3    64.6    +      -       -      +
    308A  GLU*     3.4    23.6    -      -       +      -
    309A  ILE*     4.4    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ARG*     5.8     7.9    -      -       -      +
     33A  ALA      5.3     5.8    -      -       -      +
     34A  ARG*     3.8    35.2    -      -       +      +
    281A  LEU*     3.8     9.0    -      -       -      +
    282A  GLU*     3.9    29.4    -      -       +      +
    303A  SER      4.5     2.5    -      -       -      +
    304A  TYR*     1.3    73.7    -      -       -      +
    306A  ALA*     1.3    62.6    +      -       -      +
    307A  ASP*     3.1    22.4    -      -       -      +
    308A  GLU*     3.0    35.2    +      -       +      +
    309A  ILE*     3.2    20.1    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il